[gmx-users] Re:Re: Re: Average box size
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Jan 6 10:08:23 CET 2011
Navjeet,
We're stuck with the information you give us. Apparently something's
not entirely adding up, or not matching with the way editconf
calculates the density. But don't break your head about it. I gave
another solution: calculate a scaling factor and use that with
editconf. That's completely independent of mass.
Cheers,
Tsjerk
On Thu, Jan 6, 2011 at 9:54 AM, Navjeet Ahalawat <navjeet0211 at gmail.com> wrote:
> Hi Mark,
>
> I have double check my pr.gro file It has 12348 atoms (129 protein
> residues(1960 atoms)+ 2595 Tip4p-EW water molecules upto atom # 12340+
> 8 CL ions). My protein is Lysozyme, for water definition i have pasted
> first and last water molecules.
>
> File name: pr.gro
>
> LYSOZYME in water
> 12348
> ...
> ...
> ...
> 130SOL OW 1961 1.516 0.734 1.474 -0.5687 0.1750 -0.1673
> 130SOL HW2 1962 1.565 0.744 1.392 0.7895 0.7537 0.6807
> 130SOL HW3 1963 1.521 0.821 1.514 -0.9351 -0.1981 0.6811
> 130SOL MW4 1964 1.522 0.745 1.469 -0.4629 0.1969 0.0136
> ...
> ...
> ...
> 2724SOL OW12337 -0.764 4.089 3.761 0.3226 0.7973 0.3069
> 2724SOL HW212338 -0.744 4.179 3.787 -0.5681 1.1240 -0.1194
> 2724SOL HW312339 -0.743 4.086 3.668 1.3356 0.2670 0.5421
> 2724SOL MW412340 -0.760 4.099 3.754 0.3356 0.7753 0.2868
> ...
> ...
> 2732Cl Cl12348 0.340 3.555 3.399 -0.4800 0.0112 -0.0034
> 4.44372 4.49672 4.88141 0.00000 0.00000 -1.83507 0.00000
> -1.53659 -0.46242
>
> Please tell me (if required) any other way(s) by which I can calculate
> the mass of my system.
>
> Thanks & Regards,
> Navjeet Ahalawat
>
>
> On 01/06/11, Navjeet Ahalawat <navjeet0211 at gmail.com> wrote:
>> Hi Tsjerk,
>>
>> Thanks for your more clarification, but when I am running the command
>> editconf -f pr.gro -o new_box.gro -density 1.04364e+03 (where pr.gro
>> is end.gro) the results I am getting are...
>>
>
>
> Please double check the contents of pr.gro are what you think they
> are. The simplest explanation is a file mismatch...
>
>
>>
>> Read 12348 atoms
>>
>
> Does that make sense?
>
>
>>
>> Volume: 97.5411 nm^3, corresponds to roughly 43800 electrons
>> Velocities found
>> system size : 7.244 4.992 5.194 (nm)
>> center : 0.534 2.027 2.438 (nm)
>> box vectors : 4.444 4.857 5.138 (nm)
>> box angles : 88.30 107.40 112.20 (degrees)
>> box volume : 97.54 (nm^3)
>> Volume of input 97.5411 (nm^3)
>> Mass of input 95417.2 (a.m.u.)
>> Density of input 1624.38 (g/l)
>> Scaling all box vectors by 1.1589
>> new system size : 8.395 5.785 6.019
>> new center : 0.618 2.349 2.825 (nm)
>> new box vectors : 5.150 5.628 5.955 (nm)
>> new box angles : 88.30 107.40 112.20 (degrees)
>> new box volume : 151.82 (nm^3)
>>
>> This new box volume is not matching with my average box volume
>> (97.6118). I think problem is with mass because my system (box)
>> contains 1 protein, 2595 water molecules(Tip4p-EW),and 8 CL ions. So
>>
>
> I wondered if editconf was assigning mass to TIP4P vacant sites, but
> they'd have to have mass 13.1 per solvent molecule to make that
> work...
>
> Mark
>
>
>>
>> the total mass should be 61307.332 a.m.u. (14313.332+18*2595+8*35.50)
>> and when I am calculating the density using this mass and average
>> volume (97.6118), its coming 1042.94 g/l which is approximately same
>> to average density (1.04364e+03).
>>
>> I would greatly appreciate if you could please let me know why
>> editconf is giving mass different from actual mass (my calculated
>> mass).
>>
>> Thanks & Regards,
>> Navjeet Ahalawat
>>
>>
>>
>> >Navjeet,
>>
>> >The average lengths you already mentioned in your first mail:
>>
>> >>> Box-X Box-Y Box-Z Volume Density (SI)
>> >>> 4.44479e+00 4.49781e+00 4.88259e+00 9.76118e+01 1.04364e+03
>>
>> >You also mentioned you used isotropic PC:
>>
>> >>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
>> >>> 107.40, 112.20) and Isotropic pressure coupling.
>>
>> Then the box only gets scaled during the simulation, with no changes
>> of one vector relative to the other. Then to set the box of your end
>> structure to match the average volume also means scaling. That means
>> taking the ratio of the average X-length and the actual X-length, and
>> feed that as a scaling factor...
>> Then again, you don't actually need to calculate anything, just think
>> a little bit harder. You're average box comes with an average density.
>> editconf has an option to scale the box to get a specific density, so
>> you can fetch the average density, given above and do:
>>
>> editconf -f end.gro -o average.gro -density 1.04364e+03
>>
>> Then go on with your NVT run using average.gro as input (don't forget
>> the energy minimization!).
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Tue, Jan 4, 2011 at 3:03 PM, Navjeet Ahalawat <navjeet0211 at gmail.com> wrote:
>> > Hi Tsjerk,
>> >
>> > Thanks for your clarifications. I still couldn't follow how I can calculate
>> > the scaling factor. As I wrote earlier, I ran NPT simulation for equilibration.
>> >
>> > Now to start the NVT production run, I need to know the AVERAGE LENGTHS
>> > (a, b, c) of the triclinic box vectors so that I can generate the
>> > triclinic box with the
>> > help of the corresponding angles (88.30, 107.40, 112.20) using the
>> > command "editconf".
>> >
>> > Now I understand that the box-x, box-y, and box-z represents the diagonal
>> > elements of triangular matrix and the average volume of my triclinic box
>> > is the product of these diagonal elements. However, as I understand the
>> > command "editconf" requires the length of the box vectors and the three angles
>> > to create a triclinic box.
>> >
>> > I would greatly appreciate if you could please let me know the command(s) that
>> > I would require to use to achieve my goal.
>> >
>> >
>> >
>> >
>> > Message: 4
>> > Date: Tue, 4 Jan 2011 12:35:36 +0100
>> > From: Tsjerk Wassenaar <tsjerkw at gmail.com>
>> > Subject: Re: [gmx-users] Re: Average box size
>> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> > Message-ID:
>> > <AANLkTimMYai39NMj6sv008zUuVpT_UHZAvHm=tAH34yK at mail.gmail.com>
>> > Content-Type: text/plain; charset=ISO-8859-1
>> >
>> > Hi Navjeet,
>> >
>> > These you had in the log file as you showed in your mail. Note that
>> > you use isotropic pressure coupling, so you just need to calculate a
>> > scaling factor, which you can give to editconf to change your system
>> > to match the average box size.
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> >
>> > On Tue, Jan 4, 2011 at 12:03 PM, Navjeet Ahalawat <navjeet0211 at gmail.com> wrote:
>> >> Hi Tsjerk,
>> >>
>> >> Thanks for reply, Please can you tell me how can I get the average box
>> >> length (a b c) of my triclinic box for my next step.
>> >>
>> >>> Message: 2
>> >>> Date: Mon, 3 Jan 2011 18:17:15 +0100
>> >>> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
>> >>> Subject: Re: [gmx-users] Average box size
>> >>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> >>> Message-ID:
>> >>> <AANLkTik2TYHLJVmVFC12260RqkdZnUGe-3kOKigFbM3h at mail.gmail.com>
>> >>> Content-Type: text/plain; charset="iso-8859-1"
>> >>>
>> >>> Hi Navjeet,
>> >>>
>> >>> The box is defined as a triangular matrix, so the volume equals the product
>> >>> of the diagonal elements.
>> >>>
>> >>> Hope it helps,
>> >>>
>> >>> Tsjerk
>> >>>
>> >>> On Jan 3, 2011 5:57 PM, "Navjeet Ahalawat" <navjeet0211 at gmail.com> wrote:
>> >>>
>> >>> Hi all
>> >>>
>> >>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
>> >>> 107.40, 112.20) and Isotropic pressure coupling. Now i want to use
>> >>> average box size for production run (NVT). But I am confused because i
>> >>> am not able to get the meaning of the output values of the log file.
>> >>>
>> >>>
>> >>> Log file output.....
>> >>>
>> >>> <====== ############### ==>
>> >>> <==== A V E R A G E S ====>
>> >>> <== ############### ======>
>> >>>
>> >>> Energies (kJ/mol)
>> >>> Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
>> >>> 9.31715e+02 2.35558e+03 1.63083e+02 5.15266e+03 1.79003e+03
>> >>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
>> >>> 1.63211e+04 2.86765e+04 -1.72320e+05 -4.98704e+04 -1.66800e+05
>> >>> Kinetic En. Total Energy Temperature Pressure (bar) Cons. rmsd ()
>> >>> 1.27874e+04 -1.54012e+05 1.49958e+02 1.07033e+00 0.00000e+00
>> >>>
>> >>> Box-X Box-Y Box-Z Volume Density (SI)
>> >>> 4.44479e+00 4.49781e+00 4.88259e+00 9.76118e+01 1.04364e+03
>> >>>
>> >>> If Box-X Box-Y Box-Z represent average value of a b c then volume
>> >>> does not correspond to my triclinic box because its just
>> >>> multiplication of Box-X Box-Y Box-Z. So Please can anybody help me
>> >>> which volume should I consider for next NVT production run.
>> >>>
>> >>> Any help in this regard would be highly appreciated.
>> >>>
>> >>>
>> >>> Thanks & Regards,
>> >>> Navjeet Ahalawat
>> >> --
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>> >>
>> >
>> > --
>> > Tsjerk A. Wassenaar, Ph.D.
>> >
>> > post-doctoral researcher
>> > Molecular Dynamics Group
>> > * Groningen Institute for Biomolecular Research and Biotechnology
>> > * Zernike Institute for Advanced Materials
>> > University of Groningen
>> > The Netherlands
>> >
>> >
>> > ------------------------------
>> > --
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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